how do I organize the materials? joining two seperated objects after editing
Blender only allows you to edit one object at a time, so yes you can only see and select the vertices of one object.

Every face in a model can use a different material, if you join multiple objects, the combined object will have multiple materials available and each face will continue to use the same material it used when it was in a separate object.



In edit mode you can assign a specific material to the selected faces.

If you join the multiple objects into one, you can use the by material option in the separate menu to split each into it's own object based on the material it uses.



So yes you can join multiple objects and they will keep the materials. You can easily re-separate them. You can also create one object, assign different materials to parts as you model and then separate them based on the material when you are finished.